Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens

Infection and Immunity

Volumn 71, Issue 8, 2003, Pages 4674-4683

  Anjum, Muna F ^a   Lucchini, Sacha ^b   Thompson, Arthur ^b   Hinton, Jay C D ^b   Woodward, Martin J ^a  

^a VETERINARY LABORATORIES AGENCY   (United Kingdom)

^b INSTITUTE OF FOOD RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VEROTOXIN;

ANIMAL DISEASE; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; COMPARATIVE GENOMIC INDEXING; DIARRHEA; ESCHERICHIA COLI; ESCHERICHIA COLI K 12; ESCHERICHIA COLI O26; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME ANALYSIS; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENOMICS; PRIORITY JOURNAL;

ANIMALS; BASE SEQUENCE; DNA, BACTERIAL; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; HUMANS; PHYLOGENY; SEROTYPING; SHIGA TOXINS; VARIATION (GENETICS); VIRULENCE;

EID: 0042766188     PISSN: 00199567     EISSN: None     Source Type: Journal    
DOI: 10.1128/IAI.71.8.4674-4683.2003     Document Type: Article

References (45)

1. Adu-Bobie, J., G. Frankel., C. Bain, A. G. Goncalves, L. R. Trabulsi, G. Douce, S. Knutton, and G. Dougan. 1998. Detection of intimins α, β, γ, and δ, four intimin derivatives expressed by attaching and effacing microbial pathogens. J. Clin. Microbiol. 36:662-668.
2. Behr, M. A., M. A. Wilson., W. P. Gill, H. Salamon, G. K. Schoolnik, S. Rane, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-1523.
3. Beutin, L., D. Geier, H. Steinruck, S. Zimmermann, and F. Scheutz. 1993. Prevalence and some properties of verotoxin (Shiga-like toxin)-producing Escherichia coli in seven different species of healthy domestic animals. J. Clin. Microbiol. 31:2483-2488.
4. Blattner, F. R., G. Plunkett 3rd, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
5. Caprioli, A., A. Nigrelli, R. Gatti, M. Zavanella, A. M. Blando, F. Minelli, and G. Donelli. 1993. Characterisation of verocytotoxin-producing Escherichia coli isolated from pigs and cattle in northern Italy. Vet. Rec. 133:323-324.
6. Carlioz, A., and D. Touati. 1986. Isolation of superoxide dismutase mutants in Escherichia coli: is superoxide dismutase necessary for aerobic life? EMBO J. 5:623-630.
7. Chapman, P. A., C. A. Siddons, A. T. Gerdan Malo, and M. A. Harkin. 1997. A 1-year study of Escherichia coli 0157 in cattle, sheep, pigs and poultry. Epidemiol. Infect. 119:245-250.
8. Cid, D., J. A. Ruiz-Santa-Quiteria, I. Marin, R. Sanz, J. A. Orden, R. Amils, and R. de la Fuente. 2001. Association between intimin (eae) and espB gene subtypes in attaching and effacing Escherichia coli strains isolated from diarrhoeic lambs and goat kids. Microbiology 147:2341-2353.
9. Correa, M. G., and J. M. Marin. 2002. O-serogroups, eae gene and EAF plasmid in Escherichia coli isolates from cases of bovine mastitis in Brazil. Vet. Microbiol. 85:125-132.
10. Dobrindt, U., U. Hentschel, J. B. Kaper, and J. Hacker. 2002. Genome plasticity in pathogenic and non-pathogenic enterobacteria. Curr. Top. Microbiol. Immunol. 264:157-175.
11. Dorrell, N., J. A. Mangan, K. G. Laing, J. Hinds, D. Linton, H. Al-Ghusein, B. G. Barrell, J. Parkhill, N. G. Stoker, A. V. Karlyshev, P. D. Butcher, and B. W. Wren. 2001. Whole genome comparison of Campylobacter jejuni human isolates with a low-cost microarray reveals extensive genetic diversity. Genome Res. 11:1706-1715.
12. Dziejman, M., E. Balon, D. Boyd, C. M. Fraser, J. F. Heidelberg, and J. J. Mekalanos. 2002. Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc. Natl. Acad. Sci. USA 99:1556-1561.
13. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868.
14. Fitzgerald, J. R., D. E. Sturdevant, S. M. Mackie, S. R. Gill, and J. M. Musser. 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98:8821-8826.
15. Geue, L., M. Segura-Alvarez, F. J. Conraths, T. Kuczius, J. Bockemuhl, H. Karch, and P. Gallien. 2002. A long-term study on the prevalence of shiga toxin-producing Escherichia coli (STEC) on four German cattle farms. Epidemiol. Infect. 129:173-185.
16. Gioffre, A., L. Meichtri, E. Miliwebsky, A. Baschkier, G. Chillemi, M. I. Romano, S. Sosa Estani, A. Cataldi, R. Rodriguez, and M. Rivas. 2002. Detection of Shiga toxin-producing Escherichia coli by PCR in cattle in Argentina. Evaluation of two procedures. Vet. Microbiol. 87:301-313.
17. Gunning, R. F., A. D. Wales, G. R. Pearson, E. Done, A. L. Cookson, and M. J. Woodward. 2001. Attaching and effacing lesions in the intestines of two calves associated with natural infection with Escherichia coli O26:H11. Vet. Rec. 148:780-782.
18. Guth, B. E., R. Giraldi, T. A. Gomes, and L. R. Marques. 1994. Survey of cytotoxin production among Escherichia coli strains characterised enteropathogenic (EPEC) by serotyping and presence of EPEC adherence factor (EAF) sequences. Can. J. Microbiol. 40:341-344.
19. Hiramatsu, R., M. Matsumoto, Y. Miwa, Y. Suzuki, M. Saito, and Y. Miyazaki. 2002. Characterization of Shiga toxin-producing Escherichia coli O26 strains and establishment of selective isolation media for these strains. J. Clin. Microbiol. 40:922-925.
20. + Escherichia coli isolated from healthy and diarrheic calves. Vet. Microbiol. 66:251-263.
21. Kato-Maeda, M., J. T. Rhee, T. R. Gingeras, H. Salamon, J. Drenkow, N. Smittipat, and P. M. Small. 2001. Comparing genomes within the species Mycobacteriumtuberculosis. Genome Res. 11:547-554. (Erratum, Genome Res. 11:1796.)
22. Lan, R., and P. R. Reeves. 2000. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8:396-401.
23. La Ragione, R. M., I. M. McLaren, G. Foster, W. A. Cooley, and M. J. Woodward. 2002. Phenotypic and genotypic characterisation of avian Escherichia coli O86:K61 isolates possessing a gamma-like intimin. Appl. Environ. Microbiol. 68:4932-4942.
24. Levine, M. M. 1987. Escherichia coli that cause diarrhea: enterotoxigenic, enteropathogenic, enteroinvasive, enterohaemorrhagic and enteroadherent. J. Infect. Dis. 155:377-389.
25. Maynard-Smith, J., N. H. Smith, M. O'Rourke, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
26. McGraw, E. A., J. Li, R. K. Selander, and T. S. Whittam. 1999. Molecular evolution and mosaic structure of α, β, and γ intimins of pathogenic Escherichia coli. Mol. Biol. Evol. 16:12-22.
27. Nataro, J. P., and J. B. Kaper. 1998. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11:142-201.
28. Paciorek, J. 2002. Virulence properties of Escherichia coli faecal strains isolated in Poland from healthy children and strains belonging to serogroups O18, O26, O44, O86, O126 and O127 isolated from children with diarrhoea. J. Med. Microbiol. 51:548-556.
29. Peixoto, J. C., S. Y. Bando, J. A. Ordonez, B. A. Botelho, L. R. Trabulsi, and C. A. Moreira-Filho. 2001. Genetic differences between Escherichia coli O26 strains isolated in Brazil and in other countries. FEMS Microbiol. Lett. 196:239-244.
30. Perna, N. T., G. Plunkett 3rd, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Posfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. T. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533.
31. Porter, R. D., M. W. Lark, and K. B. Low. 1981. Specialized transduction with lambda plac5: dependence on recA and on configuration of lac and att lambda. J. Virol. 38:497-503.
32. Porwollik, S., R. M. Wong, and M. McClelland. 2002. Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:8956-8961.
33. Rios, M., V. Prado, M. Trucksis, C. Arellano, C. Borie, M. Alexandre, A. Fica, and M. M. Levine. 1999. Clonal diversity of Chilean isolates of enterohemorrhagic Escherichia coli from patients with hemolytic-uremic syndrome, asymptomatic subjects, animal reservoirs, and food products. J. Clin. Microbiol. 37:778-781.
34. Salama, N., K. Guillemin, T. K. McDaniel, G. Sherlock, L. Tompkins, and S. A. Falkow. 2000. Whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc. Natl. Acad. Sci. USA 97:14668-14673.
35. Schmidt, H., M. Bielaszewska, and H. Karch. 1999. Transduction of enteric Escherichia coli isolates with a derivative of Shiga toxin 2-encoding bacteriophage φ538 isolated from Escherichia coli O157:H7. Appl. Environ. Microbiol. 65:3855-3861.
36. Sharma, V. K. 2002. Detection and quantitation of enterohemorrhagic Escherichia coli O157, O111, and O26 in beef and bovine feces by real-time polymerase chain reaction. J. Food. Prot. 65:1371-1380.
37. Smith, H. W., P. Green, and Z. Parsell. 1983. Vero cell toxins in Escherichia coli and related bacteria: transfer by phage and conjugation and toxic action in laboratory animals, chickens and pigs. J. Gen. Microbiol. 129:3121-3137.
38. Sramkova, L., M. Bielaszewska, J. Janda, K. Blahova, and O. Hausner. 1990. Vero cytotoxin-producing strains of Escherichia coli in children with haemolytic uraemic syndrome and diarrhoea in Czechoslovakia. Infection 18:204-209.
39. Tatusov, R. L., D. A. Natale, I. V. Garkavtsev, T. A. Tatusova, U. T. Shankavaram, B. S. Rao, B. Kiryutin, M. Y. Galperin, N. D. Fedorova, and E. V. Koonin. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
40. Thompson, A., S. Lucchini, and J. C. D. Hinton. 2001. It's easy to build your own Microarrayer! Trends Microbiol. 9:154-156.
41. Whittam, T. S., H. Ochman, and R. K. Selander. 1983. Multilocus genetic structure in natural populations of Escherichia coli. Proc. Natl. Acad. Sci. USA 80:1751-1755.
42. Whittam, T. S., M. L. Wolfe, I. K. Wachsmuth, F. Orskov, I. Orskov, and R. A. Wilson. 1993. Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea. Infect. Immun. 61:1619-1629.
43. Woodward, M. J., and H. P. Charles. 1982. Genes for L-sorbose utilisation in Escherichia coli. J. Gen. Microbiol. 128:1969-1980.
44. Zhang, W. L., M. Bielaszewska, A. Liesegang, H. Tschape, H. Schmidt, H. M. Bitzan, and H. Karch. 2000. Molecular characteristics and epidemiological significance of Shiga toxin-producing Escherichia coli O26 strains. J. Clin. Microbiol. 38:2134-2140.
45. Zhang, W. L., M. Bielaszewska, J. Bockemuhl, H. Schmidt, F. Scheutz, and H. Karch. 2000. Molecular analysis of H antigens reveals that human diarrheagenic Escherichia coli O26 strains that carry the eae gene belong to the H11 clonal complex. J. Clin. Microbiol. 38:2989-2993.